WASHINGTON - En route home from the Persian Gulf on a military supply ship in 2003, merchant seaman James Francis and his mates got an ultimatum: Take anthrax and smallpox vaccinations or lose your jobs.

Francis' Seattle attorney, Russell Williams, described the shipboard scene the next day off the isle of Crete as: "Wham, bam. 'Get in line. Take your shots.'"

Within days of taking the two shots, Francis' feet began to tingle and burn. When he later took the second in a series of six anthrax shots, his health slid downhill. Since then, the 45-year-old messmate from Las Vegas has fought a rare nervous system disease known as Guillain-Barre Syndrome, along with chronic pain, pneumonia and a life-threatening blood clot.

Vaccine makers are immune from lawsuits, so Francis sued the government, winning what his lawyer calls a "substantial" settlement in December 2005. Others say Uncle Sam shelled out about $2 million.

Shots for 200,000|

But Francis' success is unlikely to be duplicated by any soldier harmed in the massive anthrax inoculation program that's set to get under way in earnest early next year. Some 200,000 troops, who unlike private employees are barred from suing the U.S. government, will be required to take the vaccine.

The Pentagon is reviving its mandatory anthrax vaccinations despite allegations that the shots have contributed to as many as 23 deaths and sickened hundreds, and perhaps thousands, of soldiers.

On Tuesday, the Department of Health and Human Services canceled an $877.5 million contract with California-based VaxGen. Inc. for what would have been a substitute anthrax vaccine. HHS said the company missed deadlines for beginning tests on humans.

That puts even more focus on the controversial, decades-old vaccine, which has been used to inoculate 1.5 million military personnel. The Pentagon has been rocked by criticism that it has failed to adequately track whether the shots have caused diseases. Indeed, as occurred with Francis, many soldiers are injected with several vaccines on the same day, making it harder to identify the cause of illnesses.

In 2004, lawyers for sick soldiers won a court injunction blocking the mandatory shots until the Food and Drug Administration reviewed the license of Maryland-based vaccine manufacturer Emergent BioSolutions. In December 2005, the FDA declared the vaccine safe and restored the license.

Rare disease|

But testimony from some military doctors undercuts that decision.

Dr. Limone Collins, the medical director of the Vaccine Healthcare Center at the Army's Walter Reed Army Medical Center, testified that Francis had "a rare, vaccine-associated, neuro-immunological disease," according to court papers.

Dr. William Campbell, a neurologist at the center, said the dual vaccinations afflicted Francis with a Guillain-Barre variant in which the body's immune system attacks the nervous system.

In another case, the medical director of a Vaccine Healthcare Center at Lackland Air Force Base testified last year on behalf of Nathan Torquato, a senior airman being court-martialed for using cocaine and methamphetamine to cope with muscle pain and chronic fatigue syndrome, which he blames on his anthrax shots. Helping Torquato win a lighter sentence, Dr. David Hrncir said it "appears that we are having higher numbers of people coming down with chronic fatigue syndrome as a result of this vaccine."

Despite such testimony, Pentagon health chief William Winkenwerder announced on Oct. 16 that safety questions had been resolved and that the shots would soon resume -- the Pentagon now says in January -- for troops deployed in the Middle East, Korea and other areas at high risk of a terrorist attack with germ weapons such as smallpox and anthrax.

Vaccine deemed safe|

Col. Randall Anderson, who runs the Military Vaccine Agency, said the Pentagon believes health risks from the anthrax vaccine "are equal to those of other vaccines" that cause illnesses in only a tiny percentage of those vaccinated.

Robert Burrows, Emergent's vice president of corporate communications, pronounced the vaccine -- sold as BioThrax -- to be "safe and effective" and vetted "more than any in history."

But on Dec. 13, lawyers who succeeded in stalling the mandatory program in 2004 filed suit seeking a new injunction, alleging that the FDA manipulated data from a 1950s clinical study and circumvented its rules in licensing a vaccine that was modified multiple times.

Retired Air Force Sgt. David Lyles, 32, of Mentor, Ohio, said he was injected with the shot in October 2003 at Youngstown Air Force Base.

A few minutes later, Lyles said, he fell off a stool in the base's avionics shop from anaphylactic shock and hit his head on the cement floor. Lyles, who had always been athletic, said he recovered from the concussion but that Guillain-Barre left him walking with a cane.

"If there is a problem with the vaccine, why subject people that are helping you defend what you believe in?" asked Lyles, who also said he's lost some of his short-term memory.

An FDA system that collects adverse reaction reports for all vaccines has recorded more than 4,700 reports related to anthrax shots over the last 16 years. The number of cases, the agency says, will "inevitably be underreported."

The FDA said it has received 23 reports of anthrax vaccine-related deaths, but has seen no proof that the shots were to blame. The FDA also couldn't readily estimate the number of serious illnesses associated with the vaccinations. In the past, it has estimated 500 cases.

Dr. Meryl Nass, an internist in Bar Harbor, Maine, who has specialized in anthrax vaccine-related illnesses, says the estimates of health problems are vastly understated.

Nass said she has treated more than 500 seriously ill patients and that at least 1,500 more have phoned or sent e-mails.

Defense Department officials say several studies, including analyses of soldiers' disability claims and of post-vaccination hospitalizations, debunk the health concerns. But as recently as May, the Government Accountability Office said that the vaccine's long-term safety "has not been studied."

The Pentagon also draws criticism for giving anthrax shots with other vaccines. John Richardson, a retired Air Force pilot who has crusaded against the vaccine, charges that this is done "so they can hide which vaccine is causing the problem."

He cites the case of Rachel Lacy, a 22-year-old Army reservist who was awaiting deployment to the Persian Gulf in early 2003 when she received an anthrax shot and four other vaccinations at Fort McCoy, Wis.

A month later, she died of a pneumonia-like affliction at the Mayo Clinic in Rochester, Minn. The Pentagon called her death "a rare, tragic event that may have been related to vaccination," but said two expert medical panels couldn't identify any of the five vaccines as the culprit.

Pentagon spokeswoman Ann Ham said each reported death is similarly investigated, but none has been "causally associated with anthrax immunization alone." Anderson said a government immunization panel found no reason not to give vaccines together.

Much Pentagon data remain out of the public's reach, even though a Defense Medical Surveillance System tracks all illnesses among troops. After the National Academy of Sciences' Institute of Medicine found no proof of causal links between the vaccine and illnesses in 2002, but urged more research, the Pentagon stopped issuing quarterly analyses of BioThrax's effects. "There isn't a need for that," Anderson said.

David Geier, vice president of the Maryland-based Institute for Chronic Illnesses, and his father, Dr. Mark Geier, have analyzed the FDA's vaccine adverse reaction reports and published numerous articles on vaccine safety. David Geier said the reactions to BioThrax among healthy soldiers have been "many orders of magnitudes higher" than they've been for nearly all other civilian vaccines.

The Defense Department has said it's given the vaccine to an estimated 175,000 troops involved in the 1991 Gulf War, but said it didn't keep accurate records of who was inoculated.

A Department of Veterans Affairs advisory committee that investigated possible causes of Gulf War Syndrome, clusters of illnesses that afflicted some 200,000 war veterans, didn't rule out the anthrax vaccine as a possible cause, said Steve Robinson, a panel member and official of Veterans for America.

While Anderson said that more BioThrax studies are under way, Nass dismissed the Pentagon research as "epidemiological garbage."

For example, she cited a military study of vaccine links to optic neuritis that excluded troops who developed vision problems in their first 18 weeks in the military, even though many soldiers get their shots in boot camp. The study also omitted other soldiers not diagnosed within 18 weeks of vaccinations -- shots given just before they were sent overseas where there were no ophthalmologists, she said.

The mandatory anthrax vaccine program has been beset with problems almost since deputy FDA commissioner Michael Friedman granted a 1997 Pentagon request to expand its use from protecting people against anthrax infection in skin wounds to shielding those who breathe it.

From 1998 to 2000, hundreds of active troops, reservists and National Guardsmen risked courts-martial by refusing to take anthrax shots for fear of health problems. Then the 2004 court injunction forced the Pentagon to shift to a voluntary program. About 50 percent of troops have refused the shots.

Vaccine critics note that both the VA and the Pentagon have routinely paid disability benefits to soldiers who blame BioThrax for chronic illnesses, but they list the ailments as "service-connected" without mentioning the vaccine.

Virginia attorney Richard Stevens, who has handled a number of claims, said that way, "they always have plausible deniability."